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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNBOUND NUCLEASE DOMAIN OF COLE7
 
Authors :  Y. S. Cheng, K. C. Hsia, L. G. Doudeva, K. F. Chak, H. S. Yuan
Date :  12 Jun 02  (Deposition) - 11 Dec 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hnh Motif, Endonuclease, Colicin, Zn-Binding Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. S. Cheng, K. C. Hsia, L. G. Doudeva, K. F. Chak, H. S. Yuan
The Crystal Structure Of The Nuclease Domain Of Colicin E7 Suggests A Mechanism For Binding To Double-Stranded Dna By The H-N-H Endonucleases
J. Mol. Biol. V. 324 227 2002
PubMed-ID: 12441102  |  Reference-DOI: 10.1016/S0022-2836(02)01092-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN E7
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE70
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NUCLEASE DOMAIN
    Gene: COLE7 OR CEA
    Organism Scientific: ESCHERICHIA COLI STR. K12 SUBSTR.
    Organism Taxid: 316407
    Strain: W3110

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:544 , HIS A:569 , HIS A:573 , PO4 A:601BINDING SITE FOR RESIDUE ZN A 600
2AC2SOFTWAREARG A:447 , HIS A:544 , HIS A:545 , HIS A:569 , HIS A:573 , ZN A:600 , LYS B:576 , HOH B:811BINDING SITE FOR RESIDUE PO4 A 601
3AC3SOFTWAREHIS B:544 , HIS B:569 , HIS B:573 , PO4 B:601BINDING SITE FOR RESIDUE ZN B 600
4AC4SOFTWARELYS A:576 , HOH A:760 , ARG B:447 , HIS B:544 , HIS B:545 , HIS B:569 , HIS B:573 , ZN B:600BINDING SITE FOR RESIDUE PO4 B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M08)

(-) Exons   (0, 0)

(no "Exon" information available for 1M08)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:131
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:131
                                   455       465       475       485       495       505       515       525       535       545       555       565       575 
           CEA7_ECOLX   446 KRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
               SCOP domains d1m08a_ A: DNase domain of colicin E7                                                                                               SCOP domains
               CATH domains 1m08A00 A:446-576 Colicin e7 immunity protein. Chain B                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..........hhhhhh.....ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m08 A 446 MRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
                                   455       465       475       485       495       505       515       525       535       545       555       565       575 


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:131
                                   455       465       475       485       495       505       515       525       535       545       555       565       575 
           CEA7_ECOLX   446 KRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
               SCOP domains d1m08b_ B: DNase domain of colicin E7                                                                                               SCOP domains
               CATH domains 1m08B00 B:446-576 Colicin e7 immunity protein. Chain B                                                                              CATH domains
           Pfam domains (1) -Colicin-DNase-1m08B01 B:447-575                                                                                                  - Pfam domains (1)
           Pfam domains (2) -Colicin-DNase-1m08B02 B:447-575                                                                                                  - Pfam domains (2)
         Sec.struct. author .....ee..........hhhhhh.....ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m08 B 446 MRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
                                   455       465       475       485       495       505       515       525       535       545       555       565       575
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: His-Me_finger (38)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CEA7_ECOLX | Q47112)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

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  1m08
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  CEA7_ECOLX | Q47112
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  3.1.-.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CEA7_ECOLX | Q47112: 1mz8 1pt3 1ujz 1zns 1znv 2axc 2erh 2ivh 2jaz 2jb0 2jbg 3fbd 3gjn 3gkl 3zfk 7cei

(-) Related Entries Specified in the PDB File

1cei 1CEI CONTAINS THE CRYSTAL STRUCTURE OF THE IM7 PROTEIN
7cei 7CEI CONTAINS THE COMPLEX STRUCTURE BETWEEN THE NUCLEASE DOMAIN OF COLE7 AND ITS INHIBITOR IM7 PROTEIN